Strongbad_email.exe (2004)
(Video)
In "Anything", as Homestar pours Mountain Dew on Strong Bad's computer keyboard, he sings "Neverending soda" and hums after that both in imitation of the movie's main theme

Return of the Ghostbusters (2007)
a character refers to the ghost of Ammut looking like the ghost of Falcor from The Neverending Story

South Park: Imaginationland: Episode III (2007)
(TV Episode)
Butters reimagines the whole Imaginationland just like Bastian had to do after Fantasia had totally disappeared. Also both Butters and Bastian are characters from 'real' world.

Strongbad_email.exe: Disc Six (2008)
(Video)
In an Easter egg for "The Paper", Homestar is tangled up by printer paper and held upside-down while he sings, "The blood is rushing to my head. Blacking out, blacking out, blacking out..." to the tune of the movie's main theme

Elsewhere (2009)
The necklace that the girls wear in the film is a replica of the Auryn, which was the medallion that guided and protected Atreyu.

I'm a Celebrity, Get Me Out of Here!: Episode #12.5 (2012)
(TV Episode)
Singer Limahl talks to the younger campmates about his 80s pop hits. He mentioned he sang The NeverEnding Story theme tune. Later in the Bush Telegraph Ashley Roberts says, "The NeverEnding Story was like my old-time favourite movie growing up. I would watch the movie and then rewind it at the end to hear the song over and over again and dance in my living room like crazy. I was... I don't know I felt it was so cool that he actually was a part of that. That is my childhood."

Veep: Helsinki (2013)
(TV Episode)
The Finnish Prime Minister jokes that the furore surrounding Selina's song will become "The Never Ending Sorry".

WWE Raw: Episode #21.26 (2013)
(TV Episode)
While commenting during the Randy Orton vs. Kane match with Daniel Brian as the special guest referee, Jerry Lawler mentions this movie by name

The Amazing World of Gumball: The Routine (2015)
(TV Episode)
The scene where Richard's car gets trapped and sinks into the tar pit is a parody of a scene from that movie because Atreyu loses his horse Artax in a similar way. Also, Richard's car is named Cartax.